rs1950209

chr14-54300931-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.495 in 152,012 control chromosomes in the GnomAD database, including 19,268 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.50 (19268 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.11

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75188 AN: 151894 Hom.: 19241 Cov.: 32

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.440

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.495 AC: 75251 AN: 152012 Hom.: 19268 Cov.: 32 AF XY: 0.497 AC XY: 36898 AN XY: 74282

Gnomad4 AFR AF: 0.516

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.422

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.510

Gnomad4 FIN AF: 0.622

Gnomad4 NFE AF: 0.514

Gnomad4 OTH AF: 0.434

Alfa AF: 0.500 Hom.: 3274

Bravo AF: 0.476

Asia WGS AF: 0.319 AC: 1111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	5.5
Dann	Benign	0.45

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1950209; hg19: chr14-54767649;